Human T- and B-cell epitopes of E1 glycoprotein of rubella virus

Genetic and antigenic characterization of wild type rubella viruses isolated from India

Rubella, is a contagious disease caused by Rubella virus (RuV) that manifests as fever with skin-rashes in children and adults along with complications in pregnant women. WHO-SEAR has set a target for Rubella elimination by 2023. This is the first report of antigenic characterization and genome sequencing of nine RuVs sampled during 1992, 2007-9, and 2015-17 from four Indian states. Comparative analysis of Indian RuVs (2B) with that of global isolates and vaccine strain RA 27/3 (1a) revealed that the observed mutations in structural proteins have no major impact on the 3D structure, function and antigenicity. Indian RuVs formed three major clusters (Pune-1992, Kannur-2009 and Chitradurg-2007) in genome-based phylogeny of global isolates. Neutralizing antibody titers in a panel of serum samples from measles negative cases were significantly higher to the vaccine strain compared to a wild-type 2B isolate (Kannur) with concordance of 91.9%, thereby substantiating the use of current vaccines.

Predicting HLA CD4 Immunogenicity in Human Populations

Background

Prediction of T cell immunogenicity is a topic of considerable interest, both in terms of basic understanding of the mechanisms of T cells responses and in terms of practical applications. HLA binding affinity is often used to predict T cell epitopes, since HLA binding affinity is a key requisite for human T cell immunogenicity. However, immunogenicity at the population it is complicated by the high level of variability of HLA molecules, potential other factors beyond HLA as well as the frequent lack of HLA typing data. To overcome those issues, we explored an alternative approach to identify the common characteristics able to distinguish immunogenic peptides from non-recognized peptides.

Methods

Sets of dominant epitopes derived from peer-reviewed published papers were used in conjunction with negative peptides from the same experiments/donors to train neural networks and generate an “immunogenicity score.” We also compared the performance of the immunogenicity score with previously described method for immunogenicity prediction based on HLA class II binding at the population level.

Results

The immunogenicity score was validated on a series of independent datasets derived from the published literature, representing 57 independent studies where immunogenicity in human populations was assessed by testing overlapping peptides spanning different antigens. Overall, these testing datasets corresponded to over 2,000 peptides and tested in over 1,600 different human donors. The 7-allele method prediction and the immunogenicity score were associated with similar performance [average area under the ROC curve (AUC) values of 0.703 and 0.702, respectively] while the combined methods reached an average AUC of 0.725. This increase in average AUC value is significant compared with the immunogenicity score (p = 0.0135) and a strong trend toward significance is observed when compared to the 7-allele method (p = 0.0938). The new immunogenicity score method is now freely available using CD4 T cell immunogenicity prediction tool on the Immune Epitope Database website (http://tools.iedb.org/CD4episcore).

Conclusion

The new immunogenicity score predicts CD4 T cell immunogenicity at the population level starting from protein sequences and with no need for HLA typing. Its efficacy has been validated in the context of different antigen sources, ethnicities, and disparate techniques for epitope identification.

A novel cell-based high throughput assay to determine neutralizing antibody titers against circulating strains of rubella virus

A large rubella outbreak occurred in Japan 2013, and 14,344 rubella and 45 congenital rubella syndrome (CRS) cases were reported. At that time, the populational immunity was above the protective threshold assessed by hemmaglutination inhibition (HI) titer. The genotype 2B rubella virus (RV) strains were responsible for the outbreak, which are non-indigenous in Japan. In this work, a cell-based high throughput assay was established to measure the neutralizing antibody (NA) titer against circulating RV isolates. RV infection poorly induces cytopathic effects in tissue culture, preventing the casual measurement of NA titer. Our assay system has overcome this hurdle. Using this assay, we re-evaluated the antibody prevalence rate against circulating viral isolates using human sera collected before the outbreak. Individuals with protective IgG titer (≥10 IU/ml) represented 88.1% of the population. Consistently, 85.2% of the population had protective neutralizing antibody titers (≥1:8) against the vaccine strain. In contrast, 50.5% of the population had protective neutralizing antibody titers against circulating genotype 2B RV strains. These data suggest that the herd immunity assessed by HI titer should have been appreciated deliberately.

Study of rubella candidate vaccine based on a structurally modified plant virus

A novel rubella candidate vaccine based on a structurally modified plant virus - spherical particles (SPs) - was developed. SPs generated by the thermal remodelling of the tobacco mosaic virus are promising platforms for the development of vaccines. SPs combine unique properties: biosafety, stability, high immunogenicity and the effective adsorption of antigens. We assembled in vitro and characterised complexes (candidate vaccine) based on SPs and the rubella virus recombinant antigen. The candidate vaccine induced a strong humoral immune response against rubella. The IgG isotypes ratio indicated the predominance of IgG1 which plays a key role in immunity to natural rubella infection. The immune response was generally directed against the rubella antigen within the complexes. We suggest that SPs can act as a platform (depot) for the rubella antigen, enhancing specific immune response. Our results demonstrate that SPs-antigen complexes can be an effective and safe candidate vaccine against rubella.

Characterization of rubella virus genotypes among pregnant women in northern Vietnam, 2011-2013

Rubella virus (RV) infection is an unresolved clinical complication that affects children in developing countries including Vietnam. RV infection during the first trimester of pregnancy causes severe birth defects known as congenital rubella syndrome. This study reports on the genomic characterization of RV strains circulating in northern Vietnam during 2011-2013. RV-IgM positive amniotic fluid specimens were collected from 38 women from northern Vietnam who presented with clinical rubella at the National Hospital of Obstetrics and Gynecology in Hanoi, Vietnam. The RV genes were determined by nested PCR with primers amplifying the 739-nucleotide coding region of the E1 gene. The sequences from the amplified DNA fragments were phylogenetically analyzed and compared to reference RV strains. Seventeen out of 38 samples are positive for RV detecting. All new RV isolates are clustered to genotype 2B. Eighteen amino acid mutations were found in the T and B cell epitopes. These results suggest that genotype 2B RV strains frequently circulate in northern Vietnam. These data describe the RV genotype in Vietnam with the aim of improving maternal and child health in this country.

Rubella epidemic in Vietnam: characteristic of rubella virus genes from pregnant women and their fetuses/newborns with congenital rubella syndrome

BACKGROUND

Rubella remains poorly controlled in Southeast Asia, including Vietnam.

OBJECTIVES

The aim of this study was to characterize rubella virus spread in Vietnam during 2011-2012.

STUDY DESIGN

Amniotic fluid, throat swab and placenta samples were collected from 130 patients (110 cases from pregnant women with suspected rubella and 20 cases from fetuses/newborns). Viral RNA was obtained directly from clinical specimens, amplified by PCR, and then the E1 gene containing 739 nucleotides recommended by the WHO to identify the viral genotypes was sequenced.

RESULTS

By screening with real-time PCR, viral RNA was detectable in amniotic fluids from 103 out of 110 (93.6%) pregnant women with suspected rubella and in the throat swabs from all of 20 (100%) fetuses/newborns. In addition, viral RNA was also detected in the placenta from all cases of fetuses/newborns. All of 20 fetuses/newborns presented with congenital cataract. Twenty-four strains with the E1 gene were obtained by PCR. Using phylogenetic analysis with rubella reference sequences, all of the strains were found to be genotype 2B. Interestingly, 94% (30/32) of Vietnamese strains, including 9 strains from the database, formed an independent cluster within the genotype 2B suggesting that indigenous viruses are prevalent in this region.

CONCLUSIONS

Rubella virus identified in Vietnam belonged to the genotype 2B. Importantly, the infection rate of rubella virus in fetuses/newborns was 100% and all of them had congenital cataract. Our results indicate an establishment of rubella prevention in this area is an urgent task in order to improve maternal and child health.

Phylogenetic analysis of rubella viruses in Vietnam during 2009-2010

Rubella virus (RV) usually causes a mild disease. However, infection during the first trimester of pregnancy often leads to severe birth defects known as congenital rubella syndrome (CRS). Although wild-type RVs exist and circulate worldwide, their genotypes remain unknown in many countries. The aim of this study was to identify the molecular characteristics of RVs found in Vietnam during the years 2009-2010 and to provide the first data concerning RV genotypes in this country. Throat swab samples were collected between 2009 and 2010 from four CRS cases and nine rubella infection cases visiting one Children's Hospital and one outpatient clinic in Ho Chi Minh City. The 739-nucleotide coding region of the RV E1 gene recommended by the World Health Organization was amplified by reverse transcriptase PCR, and the resulting DNA fragments were then sequenced. Sequences were assigned to genotypes by phylogenetic analysis with RV reference strains. RV RNA was detected in 11 clinical specimens. Phylogenetic analysis of the sequences showed that all 11 strains belonged to 2B genotype. Several variations in amino acids were found, among which five changes were involved in the B and T cell epitopes. These data indicate that viruses of genotype 2B were circulating in Vietnam. The increasing information about RV genotype in Vietnam should aid in the control of rubella infection and CRS in this country.

Quantitative and qualitative assay of rubella IgA antibody in breast milk

Breast milk contains immunological factors, such as IgA antibody, which help to prevent infectious diseases. A total of 197 paired samples of colostrum and breast milk was collected from postpartum mothers in Gunma City, Japan, and examined for anti-rubella IgA antibody by enzyme-linked immunosorbent assay (ELISA) and Western blotting (WB). The anti-rubella virus IgA ranged from 0.5 to 78.5 U/ml with a mean of 6.05 U/ml and a median of 3.6 U/ml in colostrum, and from 0.5 to 32.7 U/ml with a mean of 2.74 U/ml and a median of 2 U/ml in milk. The differences between the means of titers of total IgA and anti-rubella virus IgA in colostrum and in milk were significant statistically. The levels of anti-rubella virus IgA in both colostrum and breast milk correlated positively with the anti-rubella virus hemagglutination inhibition (HI) titers in the sera of mother, indicating that the levels of these different classes of antibodies correlated. Based on WB, anti-rubella virus IgA in both colostrum and breast milk reacted with the rubella viral protein E1 and C, but not with the E2 protein.

Infection and musculoskeletal conditions: Viral causes of arthritis

Several viruses cause postinfectious arthritis. The disease is a typical manifestation of arthritogenic alphaviruses, rubella virus and human parvovirus B19. In addition, arthritis is not uncommon after infection by HIV, cytomegalovirus, hepatitis B virus, hepatitis C virus, or Epstein-Barr virus (EBV). Also prolonged arthritis may result from viral infections, particularly with alphaviruses and human parvovirus B19. Viruses such as EBV and B19 may have significant roles in initiating chronic arthropathies, which in some cases may be indistinguishable from rheumatoid arthritis.

Rubella virus nonstructural protein 2 is a minor immunogen

The full-length nonstructural protein P90 of rubella virus (RV) was expressed as recombinant protein in Escherichia coli bacteria, as well as in Vero cells. Monoclonal antibodies raised against the protein specifically reacted with the protein in both P90-transfected and RV infected Vero cells. Ninety human sera obtained from reconvalescents, vaccinees and patients with acute RV infection were tested for reactivity against the P90 protein. A weak immune reaction was detected only in a small minority (8%), indicating that P90 is minor immunogen for RV and is not suitable for diagnostic purposes.

Specific and general HLA-DR binding motifs: comparison of algorithms

Using panels of peptides well characterized for their ability to bind to HLA DR1, DRB1*1101, or DRB1*0401 molecules, algorithms were deduced to predict binding to these molecules. These algorithms consist of blocks of 8 amino acids containing an amino acid anchor (Tyr, Phe, Trp, Leu, Ile, or Val) at position i and different amino acid combinations at positions i+2 to i+7 depending on the class II molecule. The sensitivity (% of correctly predicted binder peptides) and specificity (% of correctly predicted non-binder peptides) of these algorithms, were tested against different independent panels of peptides and compared to other algorithms reported in the literature. Similarly, using a panel of 232 peptides able to bind to one or more HLA molecules as well as 43 non-binder peptides, we deduced a general motif for the prediction of binding to HLA-DR molecules. The sensitivity and specificity of this general motif was dependent on the threshold score used for the predictions. For a score of 0.1, the sensitivity and specificity were 84.7% and 69.8%, respectively. This motif was validated against several panels of binder and non-binder peptides reported in the literature, as well as against 35, 15-mer peptides from hepatitis C virus core protein, that were synthesized and tested in a binding assay against a panel of 19 HLA-DR molecules. The sensitivities and specificities against these panels of peptides were similar to those attained against the panels used to deduce the algorithm. These results show that comparison of binder and non-binder peptides, as well as correcting for the relative abundance of amino acids in proteins, is a useful approach to deduce performing algorithms to predict binding to HLA molecules.

Identification of rubella virus T-cell epitopes recognized in anamnestic response to RA27/3 vaccine: associations with boost in neutralizing antibody titer

Rubella virus (RV)-specific cell-mediated immunity (CMI) and antibodies were measured in healthy adolescents reimmunized with measles-mumps-rubella (MMR) vaccine. Lymphocyte proliferation to RV synthetic peptides was determined before and at 2, 4 and 10 weeks after, MMR. After MMR, increased CMI was observed with 16 peptides, including six containing antibody neutralization (NT) domains. Positive CMI (stimulation index > or =2.0) to E1(254-285) and C(1-29) before vaccination was significantly associated with a boost in NT titers, while positive CMI at weeks 2 or 4 to E1(254-285), E1(301-314), E1(389-408), E1(462-481), E2(134-150), E2(140-156), E2(168-179), C(1-29) and C(88-111) showed the same association.

Use of synthetic peptides to identify measles nucleoprotein T-cell epitopes in vaccinated and naturally infected humans

Recombinant measles nucleoprotein (N) and synthetic peptides spanning the length of the N-protein-coding region were used with a proliferation assay to identify human T-cell epitopes in vaccinated and naturally infected adults. A number of epitopes were mapped to specific regions of the measles virus N. The proliferative response of at least two donors was mediated by CD4(+) T cells in association with HLA DR antigens. Over 70% of all donors tested responded to peptides representing amino acids 271-290, 367-386, 400-420, and 483-502, suggesting that these peptides may be broadly recognized within an HLA diverse population. The most frequently recognized T-cell epitopes in both naturally infected and vaccinated donors were located in the genetically heterogeneous carboxy-terminal half of the N. Analysis of patterns of peptide reactivity among vaccinated and naturally infected subjects identified several regions of potential difference between these two groups. Peptides 221-240 and 237-256 were recognized among 100% of naturally infected donors but among only 37.5% of vaccinated donors and therefore may be of further interest in studies to investigate induction of lifelong versus transient immunity to measles. Use of chimeric molecules containing multiple well-characterized T- and B-cell epitopes or genetic alteration of attenuated vaccine virus to enhance critical T-cell responses may eventually lead to the development of a vaccine candidate that can more closely model the patterns of immune response elicited by wild-type virus.

Statistical comparison of established T-cell epitope predictors against a large database of human and murine antigens

Identification of T-cell epitopes within a protein antigen is an important tool in vaccine design. The T-cell epitope prediction schemes often are exploited by workers but have proved unreliable in comparison with experimental techniques. We compared published T-cell epitope predictors against two databases of human and murine T-cell epitopes. Each predictor was assessed against random cyclic permutations of epitopes in order to determine significance. Predictor performance was expressed in terms of two parameters, specificity and sensitivity. Specificity is an expression of the quality of predictions, whereas sensitivity is an expression of the quantity of epitopes predicted. Against the human data set, the strip-of-hydrophobic helix algorithm [Stille et al., Molec. Immun. 24, 1021-1027 (1987)] was the only significant predictor (p < 0.05), whereas against murine data only, the Roth2 pattern [Rothbard and Taylor, EMBO J. 7, 93-100 (1988)] was significant (p < 0.05). Not only were the majority of algorithms no better than random against both data sets, against the murine data two schemes were significant (p < 0.05) anti-predictors. This report indicates which predictors are relevant statistically and is the first to describe anti-predictors which can themselves be useful in the identification of T-cell epitopes.

Evaluation of rubella virus E2 and C proteins in protection against rubella virus in a mouse model

An animal model is described that can provide further information for evaluating novel vaccines against rubella virus (RV). A group of mice was immunized with the lysate of insect cells infected by a recombinant baculovirus expressing E2 and C proteins of RV. Another group of mice was immunized with the RA27/3 rubella vaccine. After 2 weeks, both groups of mice were challenged intramuscularly with live RV and the blood was drawn after 8, 24, 48 and 72 h. The presence of rubella challenge virus in an unnatural host, such as the mouse, was monitored by RT-PCR. The mice immunized with the RA27/3 rubella vaccine were the only ones able to inhibit the challenge virus replication, E2 and C proteins, which alone are not sufficient to protect animals against RV, served as a negative control for a protective vaccine against RV that expresses E1 protein of RV.

Expression and characterization of virus-like particles containing rubella virus structural proteins

Rubella virus (RV) virions contain two envelope glycoproteins (E1 and E2) and a capsid protein (C). Noninfectious RV-like particles (VLPs) containing three structural proteins were expressed in a BHK cell line (BHK-24S) by using an inducible promoter. These VLPs were found to resemble RV virons in terms of their size, their morphology, and some biological activities. In immunoblotting studies, VLPs were found to bind similarly to native RV virions with 10 of a panel of 12 RV-specific murine monoclonal antibodies. Immunization of mice with VLPs induced specific antibody responses against RV structural proteins as well as virus-neutralizing and hemagglutination-inhibiting antibodies. After immunization of mice with VLPs, in vitro challenge of isolated lymphocytes with inactivated RV and individual RV structural proteins stimulated proliferation. Our data suggest the possibility of using VLPs as immunogens for serodiagnostic assays and RV vaccines.

Analysis of overlapping T- and B-cell antigenic sites on rubella virus E1 envelope protein. Influence of HLA-DR4 polymorphism on T-cell clonal recognition

A CTL antigenic site located between residues 273 and 291 of the E1 envelope protein of RV was identified by 51Cr-release assays employing SPs. Two E1-specific CTL clones were examined for immune recognition of RV wild-type and attenuated vaccine strains and recombinant E1 protein. The exact sequence (273-284) recognized by both clones was delineated by using truncated and overlapping SPs covering these residues. The defined T-cell site overlapped almost completely with a virus neutralizing antibody-binding site previously identified with mouse monoclonal and human antibodies. A series of single aa-substituted SP analogues of E1(273-284) was used to define residues critical for T-cell recognition. Using EBV-BL displaying different HLA-DR haplotypes and -DR4 subtypes as targets to determine MHC class II restriction elements, immune recognition by both T-cell clones was shown to be associated with HLA-DR4. Three HLA-DR4 subtypes (DR4Dw13A, DR4Dw13B, and DR4KT2) sharing a common residue, glutamic acid at position 74 in their beta 1 chains, were able to present SP E1(273-284) to the T-cell clones.

Immunogenicity study of a synthetic T-cell epitope of rubella virus capsid protein recognized by human T cells in different strains of mice

The immunogenicity of a human immunodominant T-cell epitope C9 (residues 205-233) of rubella virus capsid protein was studied in three strains of mice using C9 lipopeptide. This peptide induced strong T-cell responses in all three strains of mice. The minimal T-cell epitope C9B (residues 205-216) recognized by human T cells with HLA-DR4 phenotype did not specifically stimulate proliferation of T cells from mice in vitro. T cells specific for C9 from immunized mice were shown to be CD4+, in agreement with results of similar studies in RV-seropositive humans.